char *getCurrentList(ListItem *list) {
char *ret;
char buffer[READ_LENGTH+1];
int fileHandle;
char *cursor;
int attempt, goodPass;
const int MAX_ATTEMPTS = 3;
buffer[READ_LENGTH] = '\0';
if (list->currentFilePosition == -1) {
list->currentFilePosition = 0;
for (attempt=0,goodPass=0;attempt < MAX_ATTEMPTS;attempt++) {
fileHandle = openList(list,NULL);
readBuffer(fileHandle,buffer,READ_LENGTH);
if (goodString(buffer,1)) {
goodPass = 1;
break;
}
close(fileHandle);
logException(30,0,0); // log failed attempt
}
if (!goodPass)
logException(30,0,RESET);
buffer[READ_LENGTH] = '\0'; //prevents readLine from searching for \n past buffer
for (cursor = buffer;*cursor != 0x0a && *cursor != 0x0d && *cursor != 0x00;cursor++);
*cursor = 0x00;
close(fileHandle);
strcpy(list->currentString,buffer);
}
ret = list->currentString;
return ret;
}
static bool export_list(int _iH5File, int *_piVar, char* _pstName, int _iVarType)
{
int iRet = 0;
bool bReturn = false;
int iItemNumber = 0;
SciErr sciErr = getListItemNumber(pvApiCtx, _piVar, &iItemNumber);
if (sciErr.iErr)
{
printError(&sciErr, 0);
return false;
}
//create groupe name
char* pstGroupName = createGroupName(_pstName);
char pstMsg[256];
sprintf(pstMsg, "list (%d)", iItemNumber);
print_type(pstMsg);
iLevel++;
//open list
void *pvList = openList(_iH5File, pstGroupName, iItemNumber);
for (int i = 0 ; i < iItemNumber ; i++)
{
int *piNewVar = NULL;
getListItemAddress(pvApiCtx, _piVar, i + 1, &piNewVar);//1 indexed
char* pstPathName = createPathName(pstGroupName, i);
if (piNewVar == NULL)
{
//undefined item
bReturn = export_undefined(_iH5File, piNewVar, pstPathName);
}
else
{
bReturn = export_data(_iH5File, piNewVar, pstPathName);
}
iRet = addItemInList(_iH5File, pvList, i, pstPathName);
FREE(pstPathName);
if (bReturn == false || iRet)
{
return false;
}
}
iLevel--;
closeList(_iH5File, pvList, _pstName, iItemNumber, _iVarType);
FREE(pstGroupName);
//close list
return true;
}
DbManager::DbManager()
: QObject() {
closingAll = false;
nconn = 0;
m_driverModel = new QStandardItemModel(this);
m_model = new QStandardItemModel(this);
lastUsedDbIndex = 0;
setupConnections();
setupModels();
openList();
}
char *getPreviousList(ListItem *list) {
char *ret;
char buffer[READ_LENGTH+1];
int fileHandle;
char *line, *tempCursor;
int attempt,goodPass;
const int MAX_ATTEMPTS = 3;
if (list->currentFilePosition == -1)
ret = getCurrentList(list);
else {
for (attempt=0,goodPass=0;attempt < MAX_ATTEMPTS && !goodPass;attempt++) {
fileHandle = openList(list,NULL);
lseek(fileHandle,list->currentFilePosition,SEEK_SET);
buffer[READ_LENGTH] = '\0'; //prevents readLine from searching for \n past buffer
getLine(-1,0); // resets DONE
line = getLine(fileHandle,buffer);
if (!line)
line[0] = 0; //empty list
else {
do {
line = getLine(fileHandle,buffer);
} while (line && strspn(line," \x0a\x0d\x00"));
if (!line) {
// end of file -- move to start
line = getLine(fileHandle,0); // to reset DONE and move to BOF
list->currentFilePosition = 0;
line = getLine(fileHandle,buffer);
if (!line)
logException(9,0,RESET); //todo: format problem with list
}
list->currentFilePosition += getFilePosition();
}
close(fileHandle);
for (tempCursor = line;*tempCursor != 0x0a && *tempCursor != 0x0d && *tempCursor != 0x00;tempCursor++);
*tempCursor = 0x00;
strcpy(list->currentString,line);
ret = list->currentString;
if ((goodPass = goodString(ret,1)))
break;
else
logException(30,0,0);
}
if (!goodPass)
logException(30,0,RESET);
}
return ret;
}
int insertIntoList(ListItem *list, long posInsert, char * string) {
//todo: create a version without a roundtrip between single/dbl-byte chars
int rHandle, wHandle, ret, i, bytesToWrite;
char wFilepath[PATH_LENGTH],rFilepath[PATH_LENGTH];
char buffer[READ_LENGTH+1];
char tempLine[LIST_ITEM_LENGTH];
int MAX_BYTES = 2 * READ_LENGTH;
strcpy(rFilepath,LIST_PATH);
strcpy(wFilepath,LIST_PATH);
strcat(wFilepath,"temp.txt");
rHandle = openList(list,rFilepath+strlen(rFilepath));
wHandle = tbOpen((LPSTR)wFilepath,O_CREAT|O_TRUNC|O_WRONLY);
ret = -1;
if (rHandle != -1 && wHandle != -1) {
buffer[READ_LENGTH] = '\0';
ret = strcspn(string,"\x0a\x0d");
if (ret > 0)
*(string + ret) = '\0';
if (posInsert) {
bytesToWrite = read(rHandle,(unsigned long)buffer << 1,posInsert % MAX_BYTES);
ret = write(wHandle,(unsigned long)buffer << 1,bytesToWrite);
for (i=bytesToWrite; i < posInsert; i+= MAX_BYTES) {
bytesToWrite = read(rHandle,(unsigned long)buffer << 1,MAX_BYTES);
ret = write(wHandle,(unsigned long)buffer << 1,bytesToWrite);
}
}
bytesToWrite = convertDoubleToSingleChar(tempLine,string,TRUE);
ret = write(wHandle,(unsigned long)tempLine<<1,bytesToWrite);
do {
bytesToWrite = read(rHandle,(unsigned long)buffer << 1,MAX_BYTES);
ret = write(wHandle,(unsigned long)buffer << 1,bytesToWrite);
} while (bytesToWrite == MAX_BYTES);
close(wHandle);
close(rHandle);
i = unlink((LPSTR)rFilepath);
if (i != -1) {
//todo: change this to rename instead of copy and unlink
i = _copy((LPSTR)wFilepath,(LPSTR)rFilepath);
if (i != -1)
i = unlink((LPSTR)wFilepath);
}
ret = i;
}
return ret;
}
char *getCurrentList(ListItem *list) {
char *ret;
char buffer[READ_LENGTH+1];
int fileHandle;
char *cursor, *cp;
int attempt, goodPass;
ListItem *masterlist;
const int MAX_ATTEMPTS = 3;
buffer[READ_LENGTH] = '\0';
if (list->currentFilePosition == -1) {
list->currentFilePosition = 0;
for (attempt=0,goodPass=0;attempt < MAX_ATTEMPTS;attempt++) {
fileHandle = openList(list,NULL);
readBuffer(fileHandle,buffer,READ_LENGTH);
if (goodString(buffer,1)) {
goodPass = 1;
break;
}
close(fileHandle);
logException(30,0,0); // log failed attempt
}
if (!goodPass)
logException(30,0,RESET);
buffer[READ_LENGTH] = '\0'; //prevents readLine from searching for \n past buffer
for (cursor = buffer;*cursor != 0x0a && *cursor != 0x0d && *cursor != 0x00;cursor++);
*cursor = 0x00;
close(fileHandle);
//device-58
masterlist = &pkgSystem.lists[context.package->idxMasterList];
list->isLocked = 0;
cp = buffer;
if(list == masterlist) {
if(*buffer == '!') { // catagory locked, no writing allowed
list->isLocked = 1;
cp++;
}
}
//device-58
strcpy(list->currentString,cp);
}
ret = list->currentString;
return ret;
}
void Search::doSearch(char* words) {
struct timeval start, end;
gettimeofday(&start, NULL);
cout<<"do searching...."<<endl<<" key words:"<<words<<endl;
//for(int i =0; i< key_words.size();i++)
// cout<<key_words[i]<<" ";
result_count = 0;
int request_count = 0;
string word="";
int pos=0;
int N = (int)docMap.size();
vector<string> request_list;
// while(get_one_word(words,pos,word))
// {
// cout<<"new:"<<word<<endl;
// request_list.push_back(word);
// request_count++;
// word="";
//
// }
stringstream ss;
ss << words;
string temp;
while (ss >> temp) {
request_list.push_back(temp);
request_count ++;
}
if(request_count == 0)
return;
vector<LP*> p;
// _result.print();
for(int i = 0 ; i < request_list.size();i++)
{
int word_id=lexMap[request_list[i]];
cout<<"word: "<<request_list[i]<<" word_id:"<<word_id<<endl;
if(word_id == 0)
continue;
LP* tmp = openList(word_id);
if(tmp == NULL)
continue;
p.push_back(tmp);
}
if(p.size() == 0)
return;
cout<<"p.size:"<<p.size()<<endl;
cout<<"doc_map_size: "<<docMap.size()<<endl;
int did = 0;
while(did < N)
{
int d = 0;
did = nextGEQ(p[0],did);
// if( did == 0)
// {
// cout<<"did = 0"<<endl;
// continue;
// }
for(int i = 1; (i< p.size())&& ((d=nextGEQ(p[i],did))==did);i++);
if(did> N)
break;
if(d > did) did = d-1;
else
{
float bm25_all = 0.0;
STRU_DOC one_doc = docMap[did];
//cout<<"doc_id:"<<did<<"url:"<<one_doc.doc_name<<" file: "<<one_doc.file_id<<" offset:"<<one_doc.offset<<" len:"<<one_doc.len<<endl;
//int target_pos = getPos(p[0]);
for( int k = 0 ; k<p.size(); k++)
{
int freq= getFreq(p[k]);
int ft=p[k]->doc_num;
if(one_doc.doc_name == "")
continue;
//cout<<"doc_id:"<<did<<"url:"<<one_doc.doc_name<<" file: "<<one_doc.file_id<<" offset:"<<one_doc.offset<<" len:"<<one_doc.len<<endl;
//cout<<"req:"<<freq<<" ft:"<<ft<<endl;
//comput bm25
float K = (float)k1 * (float)((1-b) + b* ((float)one_doc.len / (float)d_agv ) );
float bm25 = log ( (float)(N-ft+0.5)/(float)(ft+0.5) ) * ((k1 + 1)*(float)freq)/(float)(K + freq);
//cout<<"bm25:"<<bm25<<endl;
bm25_all+=bm25;
}
if(result_count < 10)
{
STRU_RESULT temp;
temp._url =one_doc.doc_name;
temp._bm25=bm25_all;
temp._doc_id = did;
//temp._pos = target_pos;
result_array.push(temp);
result_count++;
}
else if(bm25_all > result_array.top()._bm25)
{
STRU_RESULT temp;
temp._url =one_doc.doc_name;
temp._bm25=bm25_all;
temp._doc_id = did;
//temp._pos = target_pos;
result_array.pop();
result_array.push(temp);
}
//sort(result_array,0,result_count-1);
}
//cout<<"list:";
//for(int j =0; j < result_count; j++)
// cout<<"["<<j<<"] "<<result_array[j]._bm25<<endl;
did++;
}
gettimeofday(&end, NULL);
_searching_time = (end.tv_sec - start.tv_sec)*1000+ (end.tv_usec - start.tv_usec)/1000.0;
}
char *getNextList(ListItem *list, BOOL shouldAdvance) {
char *ret;
char buffer[READ_LENGTH+1];
int fileHandle;
char *line, *tempCursor;
int cursor;
long position, bytesToRead;
int attempt, goodPass;
ListItem *masterlist;
const int MAX_ATTEMPTS = 3;
for (attempt=0,goodPass=0;attempt < MAX_ATTEMPTS && !goodPass;attempt++) {
position = list->currentFilePosition;
if (position == -1 || position == 0) {
fileHandle = openList(list,NULL);
position = 0;
// find last entry in file
while (readBuffer(fileHandle,buffer,READ_LENGTH))
position += READ_LENGTH;
if (buffer[0]) { //check not empty list
//move before any empty last line, although this file should be machine-written
for (line=strchr(buffer,0)-1;isspace(*line) && line > buffer;line--);
cursor = line - buffer;
}
}
else if (shouldAdvance) {
fileHandle = openList(list,NULL);
bytesToRead = 80;
if (position < bytesToRead) { //todo: move this to #define and make sure it is < READ_LENGTH
bytesToRead = position;
position = 0;
}
else {
position -= bytesToRead;
lseek(fileHandle,position,SEEK_SET);
}
readBuffer(fileHandle, buffer, bytesToRead);
for (cursor = bytesToRead-1;buffer[cursor]==0x0a || buffer[cursor]==0x0d || isspace(buffer[cursor]);cursor--);
buffer[cursor+1] = '\0';
}
if (buffer[0] && (shouldAdvance || (position == -1 || position == 0))) {
for (;cursor > 0 && buffer[cursor-1] != 0x0a && buffer[cursor-1] != 0x0d; cursor--);
for (tempCursor = &buffer[cursor];*tempCursor != 0x0a && *tempCursor != 0x0d && *tempCursor != 0x00;tempCursor++);
*tempCursor = 0x00;
position += cursor;
list->currentFilePosition = position;
//device-58
masterlist = &pkgSystem.lists[context.package->idxMasterList];
list->isLocked = 0;
if(list == masterlist) {
if(*(buffer+cursor) == '!') { // catagory locked, no writing allowed
list->isLocked = 1;
cursor++;
}
}
//device-58
strcpy(list->currentString,&buffer[cursor]);
goodString(list->currentString,1);
close(fileHandle);
}
if (!buffer[0])
list->currentString[0] = 0;
ret = list->currentString;
if ((goodPass = goodString(ret,1)))
break;
else
logException(30,0,0);
}
if (!goodPass)
logException(30,0,RESET);
return ret;
}
AViz::AViz()
: QMainWindow()
{
// Make menus in menubar
QMenu *file = menuBar()->addMenu("&File");
QMenu *elements = menuBar()->addMenu( "&Elements");
QMenu *view = menuBar()->addMenu( "&View");
QMenu *settings = menuBar()->addMenu( "&Settings");
QMenu *data = menuBar()->addMenu("&Data");
menuBar()->addSeparator();
QMenu *help = menuBar()->addMenu("&Help");
// Make a cascade menu to read files
QMenu *openfile = file->addMenu("&Open");
openfile->addAction("Open XYZ File...", this, SLOT(openXYZ()));
openfile->addAction("Open File List...", this, SLOT(openList()));
openfile->addAction("Open ViewParam File...", this, SLOT(openViewParam()));
file->addAction( "Save ViewParam File...", this, SLOT(saveViewParam()) );
file->addSeparator();
file->addAction( "File List...", this, SLOT(launchFileList()) );
file->addAction( "Animation...", this, SLOT(launchAnimation()) );
file->addSeparator();
m_inOutWatchModelAction = file->addAction( "Watch XYZ File", this, SLOT(watchFile()) );
file->addSeparator();
file->addAction( "Snap PNG File...", this, SLOT(savePNGFile()) );
file->addSeparator();
file->addAction( "Set Default View Param", this, SLOT(setDefaultView()));
file->addSeparator();
file->addAction( "E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q );
// Make a general view menu
QMenu *viewpoint = view->addMenu("Set &Viewpoint");
view->addAction( "Clipping...", this, SLOT(launchClip()) );
view->addAction( "Slicing...", this, SLOT(launchSlice()) );
// Make a cascade menu to set standard view points
viewpoint->addAction( "Explicit...", this, SLOT(launchExplicit()) );
viewpoint->addSeparator();
viewpoint->addAction( "Default View", this, SLOT(setDefaults()) );
viewpoint->addSeparator();
viewpoint->addAction( "View XY +", this, SLOT(viewXYPlus()) );
viewpoint->addAction( "View XY -", this, SLOT(viewXYMinus()) );
viewpoint->addSeparator();
viewpoint->addAction( "View XZ +", this, SLOT(viewXZPlus()) );
viewpoint->addAction( "View XZ -", this, SLOT(viewXZMinus()) );
viewpoint->addSeparator();
viewpoint->addAction( "View YZ +", this, SLOT(viewYZPlus()) );
viewpoint->addAction( "View YZ -", this, SLOT(viewYZMinus()) );
// Fill a general elements menu
m_atomsMenu = elements->addMenu("Atoms...");
// Make a submenu for atom specifications
m_atomsMenu->addAction( "Atoms/Molecules...", this, SLOT(launchAtoms()) );
m_atomsMenu->addAction( "Bonds...", this, SLOT(launchBonds()) );
m_spinsAction = elements->addAction( "Spins...", this, SLOT(launchSpins()) );
m_liquidCrystalsAction = elements->addAction( "Liquid Crystals...", this, SLOT(launchLiquidCrystals()) );
m_polymersMenu = elements->addMenu( "Polymers...");
m_poresAction = elements->addAction( "Pores ...", this, SLOT(launchPores()) );
elements->addAction( "Lights...", this, SLOT(launchLights()) );
elements->addAction( "Annotation...", this, SLOT(launchAnnotation()) );
// fill submenu for polymer specifications
m_polymersMenu->addAction( "Polymers...", this, SLOT(launchPolymers()) );
m_polymersMenu->addAction( "Bonds...", this, SLOT(launchBonds()) );
// fill a general settings menu
m_showHideAxesAction = settings->addAction( "Hide Axes", this, SLOT(showHideAxesCB()) );
m_showHideContourAction = settings->addAction( "Hide Contour", this, SLOT(showHideContourCB()) );
m_onlyContourAction = settings->addAction( "Only Contour", this, SLOT(onlyContourCB()) );
// fill a general data menu
data->addAction( "&Translate...", this, SLOT(launchTranslation()) );
data->addSeparator();
data->addAction( "Swap XY", this, SLOT(swapXY()) );
data->addAction( "Swap XZ", this, SLOT(swapXZ()) );
data->addAction( "Swap YZ", this, SLOT(swapYZ()) );
data->addSeparator();
data->addAction( "Mirror X", this, SLOT(mirrorX()) );
data->addAction( "Mirror Y", this, SLOT(mirrorY()) );
data->addAction( "Mirror Z", this, SLOT(mirrorZ()) );
data->addSeparator();
data->addAction( "Stretch XYZ...", this, SLOT(launchStretch()) );
// fill a general help menu
help->addAction( "&About", this, SLOT(about()), Qt::CTRL+Qt::Key_H );
help->addAction( "License", this, SLOT(license()) );
help->addAction( "Distribution", this, SLOT(distribute()) );
// Now construct the main form
// (Note having aviz as paramter for MainForm ctor
// is "This is an ugly hack, intended to propagate the
// address of the calling class")
m_mainForm = new MainForm(this/*parent*/, this /*aviz*/);
setCentralWidget(m_mainForm);
// Construct a timer
m_watchTimer = new QTimer(this);
// Set initial settings
setAtomMenus();
}
path*
FlexibleAStar::search(node* start, node* goal)
{
nodesExpanded=0;
nodesTouched=0;
searchTime =0;
nodesGenerated = 0;
if(verbose)
{
std::cout << "getPath() mapLevel: ";
std::cout <<start->getLabelL(kAbstractionLevel)<<std::endl;
}
if(!checkParameters(start, goal))
return NULL;
start->setLabelF(kTemporaryLabel, heuristic->h(start, goal));
start->backpointer = 0;
altheap openList(heuristic, goal, 30);
std::map<int, node*> closedList;
openList.add(start);
path *p = NULL;
Timer t;
t.startTimer();
while(1)
{
node* current = ((node*)openList.remove());
// check if the current node is the goal (early termination)
if(current == goal)
{
closeNode(current, &closedList);
p = extractBestPath(current);
if(verbose)
debug->printNode(std::string("goal found! "), current);
break;
}
// expand current node
expand(current, goal, &openList, &closedList);
closeNode(current, &closedList);
// terminate when the open list is empty
if(openList.empty())
{
if(verbose) std::cout << "search failed. ";
break;
}
}
searchTime = t.endTimer();
closedList.clear();
start->drawColor = 3;
goal->drawColor = 3;
if(verbose)
{
std::cout << "\n";
debug->printPath(p);
}
return p;
}